[BioC] How to generate the CDF files for Arabidopsis TilingArrays

[Al Ivens]

Hi Naira,

Quick question re the CDF.  Was this made using TAIR release 8 or
release 7 gene set?  If 7, do you have any plans to generate one for
release 8?

Many thanks,

Al

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Naira Naouar
> Sent: 04 March 2009 08:58
> To: zhen tao
> Cc: Bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] How to generate the CDF files for 
> Arabidopsis TilingArrays
> 
> 
> Hi Zhen,
> 
> 
> The Arabidopsis tiling 1.0R cdf that I generated is available 
> here: ftp://ftp.psb.ugent.be/pub/nanao/athtiling1.0rcdf_1.0.1.tar.gz
> 
> this CDF contains 29670 probesets and was created on a unix 
> environment.
> 
> If you are analysing tiling arrays in R, you must make sure 
> that you have enough memory available To make use of the 
> package those are the instructions: In R:
> 
> library(affy)
> library(athtiling1.0rcdf)
> data<-ReadAffy()
> data at cdfName<-"athtling1.0rcdf"
> 
> Then use rma or mas5 to preprocess your data (gcrma is not 
> possible because I did not create the probe file).
> 
> Good luck with your analysis.
> If you have any problem with the package (installation or 
> any), feel free to contact me. To install a R package in 
> unix, : R CMD INSTALL 
> athtiling1.0rcdf_1.0.1.tar.gz /path/R/libraries
> 
> Best,
> Naira
> 
> 
> zhen tao wrote:
> > Dear all,
> >
> > I'm new to R programming and Bioconductor. Recently I'm trying to 
> > analyze the data of Arabidopsis Tiling Array using Bioconductor. 
> > However, I noticed that the CDF files should be included when 
> > importing the CEL files so that we can do the QC or RMA 
> studies. But 
> > there's no cdf/probe package files for this tiling array ( only for 
> > ATH1). I have downloaded the files named 
> > attltiling10rattaircdf_10.0.0.tar and 
> attltiling10rattairprobe_10.0.0.tar
> > somewhere. May I know if these files can be used as the 
> tiling array cdf
> > since the R keeps displaying the message
> >  Error in getCdfInfo(object) :
> >   Could not obtain CDF environment, problems encountered:
> > Specified environment does not contain At35b_MR_v04
> > Library - package at35bmrv04cdf not installed
> > Bioconductor - at35bmrv04cdf not available
> >
> > If not, is there anyway I can do to generate the cdf file for this 
> > tiling array?
> >
> > thanks,
> > Tao Zhen
> >
> > 	[[alternative HTML version deleted]]
> >
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> >   
> 
> 
> -- 
> ==================================================================
> Naïra Naouar 
> 
> Tel:+32 (0)9 331 38 63
> VIB Department of Plant Systems Biology, Ghent University 
> Technologiepark 927, 9052 Gent, BELGIUM
> nanao at psb.vib-ugent.be                         
> http://www.psb.vib-ugent.be
> 
> 
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